package jalview.ws.jws2.jabaws2;

import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
import jalview.ws.api.CancellableI;
import jalview.ws.api.JobId;
import jalview.ws.api.MultipleSequenceAlignmentI;
import jalview.ws.gui.WsJob;
import jalview.ws.gui.WsJob.JobState;
import jalview.ws.jws2.JabaParamStore;
import jalview.ws.jws2.JabaPreset;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.InvalidArgumentException;
import jalview.ws.params.WsParamSetI;

import java.io.IOError;
import java.rmi.ServerError;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import compbio.data.msa.MsaWS;
import compbio.data.sequence.Alignment;
import compbio.data.sequence.FastaSequence;
import compbio.metadata.Argument;
import compbio.metadata.ChunkHolder;
import compbio.metadata.JobStatus;
import compbio.metadata.Preset;
import compbio.metadata.ResultNotAvailableException;

public class JabawsMsaInstance
        implements MultipleSequenceAlignmentI, CancellableI
{
  /**
   * our service instance handler generated by the discoverer
   */
  Jws2Instance our;

  MsaWS<?> service;

  @Override
  public JobId align(List<SequenceI> toalign, WsParamSetI parameters,
          List<ArgumentI> arguments) throws Throwable
  {
    List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
    for (SequenceI seq : toalign)
    {
      seqs.add(new FastaSequence(seq.getName(), seq.getSequenceAsString()));
    }
    String jobid = null;
    if (parameters != null)
    {
      if (parameters instanceof JabaPreset)
      {
        jobid = service.presetAlign(seqs,
                ((JabaPreset) parameters).getJabaPreset());
      }
      else
      {
        jobid = service.customAlign(seqs, JabaParamStore
                .getJabafromJwsArgs(parameters.getArguments()));
      }
    }
    else if (arguments != null && arguments.size() > 0)
    {
      jobid = service.customAlign(seqs,
              JabaParamStore.getJabafromJwsArgs(arguments));
    }
    else
    {
      jobid = service.align(seqs);
    }

    if (jobid == null)
    {
      return null;
    }
    return new JobId(our.getServiceType(), our.getName(), jobid);
  }

  @Override
  public AlignmentI getAlignmentFor(JobId jobId)
          throws InvalidArgumentException, ServerError, IOError
  {
    Alignment alignment = null;
    try
    {
      alignment = service.getResult(jobId.getJobId());
    } catch (ResultNotAvailableException rnotav)
    {

      // TODO - migrate JABA exception
      // throw new ServerError("Couldn't get result for job",rnotav);
    }
    SequenceI[] alseqs;
    int alseq_l = 0;
    if (alignment.getSequences().size() == 0)
    {
      return null;
    }

    alseqs = new SequenceI[alignment.getSequences().size()];
    for (compbio.data.sequence.FastaSequence seq : alignment.getSequences())
    {
      alseqs[alseq_l++] = new Sequence(seq.getId(), seq.getSequence());
    }
    AlignmentI jv_al = new jalview.datamodel.Alignment(alseqs);
    jv_al.setGapCharacter(alignment.getMetadata().getGapchar());
    return jv_al;

  }

  public JabawsMsaInstance(Jws2Instance handle)
  {
    our = handle;
    service = (MsaWS<?>) our.service;
  }

  @Override
  public boolean cancel(WsJob job)
  {
    service.cancelJob(job.getJobId());
    // if the Jaba server indicates the job can't be cancelled, its
    // because its running on the server's local execution engine
    // so we just close the window anyway.

    return true;
  }

  Map<JobStatus, JobState> jwsState = new HashMap<>();
  {
    jwsState.put(JobStatus.CANCELLED, JobState.CANCELLED);
    jwsState.put(JobStatus.COLLECTED, JobState.FINISHED);
    jwsState.put(JobStatus.FAILED, JobState.FAILED);
    jwsState.put(JobStatus.FINISHED, JobState.FINISHED);
    jwsState.put(JobStatus.PENDING, JobState.QUEUED);
    jwsState.put(JobStatus.RUNNING, JobState.RUNNING);
    jwsState.put(JobStatus.STARTED, JobState.RUNNING);
    jwsState.put(JobStatus.SUBMITTED, JobState.SUBMITTED);
    jwsState.put(JobStatus.UNDEFINED, JobState.UNKNOWN);
  }
  @Override
  public void updateStatus(WsJob job)
  {
    JobStatus jwsstatus = service.getJobStatus(job.getJobId());
    job.setState(jwsState.get(jwsstatus));
  }

  @Override
  public boolean updateJobProgress(WsJob job) throws Exception
  {
    StringBuilder response = new StringBuilder(job.getStatus());
    long lastchunk = job.getNextChunk();
    boolean changed = false;
    do
    {
      ChunkHolder chunk = service.pullExecStatistics(job.getJobId(),
              lastchunk);
      if (chunk != null)
      {
        changed |= chunk.getChunk().length() > 0;
        response.append(chunk.getChunk());
        lastchunk = chunk.getNextPosition();
        try
        {
          Thread.sleep(50);
        } catch (InterruptedException x)
        {
        }
        ;
      }
      ;
      job.setnextChunk(lastchunk);
    } while (lastchunk >= 0 && job.getNextChunk() != lastchunk);
    if (job instanceof WsJob)
    {
      // TODO decide if WsJob will be the bean for all ng-webservices
      job.setStatus(response.toString());
    }
    return changed;
  }

  public boolean isPresetJob(WsJob job)
  {
    return job.getPreset() != null && job.getPreset() instanceof JabaPreset;
  }

  public Preset getServerPreset(WsJob job)
  {
    return (isPresetJob(job))
            ? ((JabaPreset) job.getPreset()).getJabaPreset()
            : null;
  }

  public List<Argument> getJabaArguments(WsParamSetI preset)
  {
    List<Argument> newargs = new ArrayList<>();
    if (preset != null)
    {
      if (preset instanceof JabaWsParamSet)
      {
        newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
      }
      else
      {
        newargs.addAll(
                JabaParamStore.getJabafromJwsArgs(preset.getArguments()));
      }
    }
    return newargs;
  }

  @Override
  public boolean handleSubmitError(Throwable _lex, WsJob j,
          WebserviceInfo wsInfo) throws Exception, Error
  {
    if (_lex instanceof compbio.metadata.UnsupportedRuntimeException)
    {
      wsInfo.appendProgressText(MessageManager.formatMessage(
              "info.job_couldnt_be_run_server_doesnt_support_program",
              new String[]
              { _lex.getMessage() }));
      wsInfo.warnUser(_lex.getMessage(),
              MessageManager.getString("warn.service_not_supported"));
      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
      wsInfo.setStatus(j.getJobnum(),
              WebserviceInfo.STATE_STOPPED_SERVERERROR);
      return true;
    }
    if (_lex instanceof compbio.metadata.LimitExceededException)
    {
      wsInfo.appendProgressText(MessageManager.formatMessage(
              "info.job_couldnt_be_run_exceeded_hard_limit", new String[]
              { _lex.getMessage() }));
      wsInfo.warnUser(_lex.getMessage(),
              MessageManager.getString("warn.input_is_too_big"));
      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
      wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
      return true;
    }
    if (_lex instanceof compbio.metadata.WrongParameterException)
    {
      wsInfo.warnUser(_lex.getMessage(),
              MessageManager.getString("warn.invalid_job_param_set"));
      wsInfo.appendProgressText(MessageManager.formatMessage(
              "info.job_couldnt_be_run_incorrect_param_setting",
              new String[]
              { _lex.getMessage() }));
      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
      wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
      return true;
    }
    // pass on to generic error handler
    return false;
  }

  @Override
  public boolean handleCollectionException(Exception ex, WsJob msjob,
          WebserviceInfo wsInfo)
  {
    if (ex instanceof compbio.metadata.ResultNotAvailableException)
    {
      // job has failed for some reason - probably due to invalid
      // parameters
      Cache.log.debug(
              "Results not available for finished job - marking as broken job.",
              ex);
      String status = msjob.getStatus();

      msjob.setStatus(status
              +
              "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
                      + ex.getLocalizedMessage());
      msjob.setState(WsJob.JobState.BROKEN);
      return true;
    }
    return false;
  }
}